Mapping QC

Column

Global mapping statistics

Total_Pairs 234252877 100%
Total_Pairs_Mapped 232469423 99.2%
Total_Uniq_Mapped 220128641 94%
Total_Mito_Mapped 498673 0.2%
Total_Dups 98905770 42.2%
Total_Pairs_MAPQ30 215331878 91.9%
Total_Mito_MAPQ30 397362 0.2%
Total_Dups_MAPQ30 94300385 40.3%

Column

Mapping statistics for cell barcodes

Cell called by FILTER
Estimated # of cells 6788
Fraction of MAPQ30 in cells 65.6%
Median fragments per cell 11542
Library Complexity (non redudant fraction) 55.2%

Cell barcodes QC

Row

TSS enrichment score profile

Overlapping with sequence annotated regions

Overlapping statistics

Fraction in peaks 68.1%
Fraction in mitocondrial chromosome 0.1%
Fraction in promoters 45.5%
Fraction in Enhancers(ENCODE) 23.7%
Fraction in TSS 39.3%

Row

Distribution of fragments

Total fragments VS fraction in peaks

Distribution of Insert Size

Downstream Analysis

Column

Clustering

Total reads per cell

Column

Motif Analysis

Column

Footprinting Analysis: Comparing two clusters

An example